Wednesday, June 30, 2010

Bicycle helmets can only protect people's heads if they are completely undamaged. But how can you tell whether dropping your helmet a few times is enough to compromise its safety? If Christof Koplin and other scientists at the Fraunhofer Institute have their way, you’ll be able to smell the difference.

The researchers placed bad-smelling oils within microcapsules. These tiny capules, each no more than 50 micrometers long, are sealed within a layer of melamine formaldehyde resin and then embedded within the polypropylene portion of the helmet. The resin prevents the capsules from rupturing during the manufacturing process or minor wear and tear. If the helmet is structurally damaged, however, they begin to break. The worse the damage, the worse the resulting smell.

Apart from helmets, the researchers envision using their smell detection system in otherwise inaccessible hoses and pipes.

Tuesday, June 29, 2010

Trekking pole manufacturers maintain that their poles can greatly reduce the forces on lower limb joints. Glyn Howatson of Northumbria University tested that claim and found evidence to support it.

In the study, 37 participants volunteered to hike up and down Snowdon (the highest peak in England and Wales) either with or without the aid of trekking poles. Those who used the poles were trained in their proper usage before setting out. The two groups ate the same meals before and after hiking, and took the same rest stops.

Both prior to and during the hike, heart rates and perceived levels of exertion were recorded. At 0, 24, 48 and 72 hours after the completion of the hike, muscle damage was assessed. The volunteers who used trekking poles had significantly less muscle soreness and less creatine kinase (an enzyme marker for muscle damage).

According to Howatson:

The results present strong evidence that trekking poles reduce, almost to the point of complete disappearance, the extent of muscle damage during a day's mountain trek.

To me, walking sticks always seemed like one more heavy thing to drag along on a hike. Apparently, they can actually lighten the load.

Monday, June 28, 2010

Cosmologists have found hundreds of extrasolar (outside of our solar system) planets. They’re still looking for ones that might be habitable and that might even host alien civilizations. New computer models developed by Rory Barnes of the University of Washington show that those planets may be even more rare than previously thought.

In order to sustain life, a planet must orbit its star in what’s termed the ‘habitable zone’, the zone at which liquid water is available. If a planet orbits a star alone, it’s likely to remain in a stable orbit with limited temperature fluctuations. The addition of other planets to the system, particularly gas giants such as Jupiter, could give those smaller rocky planets extremely elliptical orbits. Such a planet might spend part of every thousand years in the habitable zone, and the rest in a region of space where all water either boils away or freezes solid.

While this doesn’t preclude the possibility of finding life on such planets, it does pretty much rule out intelligent life, let alone civilization, which wouldn’t have had enough time to evolve. To be clear, this new model simply shows that if we find what appears to be a habitable planet, it might not have been in the habitable zone just a few centuries earlier. It doesn’t mean that there can’t be long-term life-sustaining planets just like Earth out there somewhere. In the meantime, astronomers will continue to search.

Sunday, June 27, 2010

Mad Cow Disease (bovine spongiform encephalopathy) is a fatal disease that can infect humans who consume beef. For this reason, it’s critical to identify the cows that suffer from this disease before they are sent to market. So far, Jacob Petrich and his colleagues from Iowa State and the University of Pittsburgh have found a test that seems to work in sheep.

The researchers used fluorescence spectroscopyto examine the eyes of sheep suffering from a similar transmissible spongiform encephalopathy known as ‘scrapie’. The infected sheep’s eyes emitted a specific glow that was not visible in uninfected sheep retinas. This quick, noninvasive test would be of tremendous use to the meat industry, especially if it also works in cattle. The meat supply would be that much safer for all of us.

Saturday, June 26, 2010

Everyone knows that if you feel tired, a cup of coffee will pick you up.Or will it?In one recent test, Peter Rogers and his colleagues from the Universities of Bristol, Münster, and Würzburg and from Imperial College London have determined that, contrary to popular opinion, caffeine does not increase alertness.

379 people who had abstained from caffeine for 16 hours were given either a placebo or caffeine.About half of the participants ranked themselves as non/low caffeine users, the other half as medium/high users. They were all questioned about perceived levels of alertness, headache and anxiety both before and after being given their unknown nostrum.In addition, they were physically tested for levels of alertness.

Although the medium/high users reported increased headache and dullness with placebo as compared to with caffeine, their tested level of alertness on caffeine was similar to that of the non/low users on placebo.In other words, the caffeine users were only as alert with caffeine as the nonusers were without it.

The authors interpret this result as meaning that the medium/high caffeine users had been suffering from caffeine withdrawal, and that adding caffeine back after the 16 hour caffeine fast merely brought their alertness levels back up to normal.The nonusers, having suffered no caffeine withdrawal, maintained the same alertness level with or without caffeine.

If these results are true, this implies that people get no benefit beyond placebo when they first start using caffeine as a stimulant, but that they subsequently require caffeine to prevent withdrawal symptoms. Anecdotally, I never found my caffeine consuming friends to be any more alert than my non-caffeine using self.

Friday, June 25, 2010

Could life exist on Mars? Now that researchers have discovered bacteria in regions of Earth that are more inhospitable than Mars, that possibility becomes more likely.

The Lost Hammer Spring on Axel Heiberg Island, in the extreme north of Canada, is about as inhospitable as you can get. The water in the spring is so salty that it doesn’t freeze even at the -50ºC often experienced in the area. While the water contains no detectable oxygen, it does have large bubbles of methane emanating from it. Lyle Whyte and his colleagues from McGill University, the University of Toronto and the SETI institute, discovered some unique methane-eating anaerobic bacteria in the salty frigid waters.

While Mars does not resemble Earth in great detail, it does have both methane and frozen water. In places, the temperature even reaches a balmy -10ºC or higher. So who knows? Exobiologists are continuing to search for life there.

Wednesday, June 23, 2010

Knee pain, or more specifically, patellofemoral pain (PFP), is one of the most common injuries incurred by female runners. Tracy Dierks and his colleagues at Indiana University-Purdue University Indianapolis have hit upon one possible treatment: a series of exercises designed to strengthen runners’ hips.

Typically, a PFP sufferer begins to feel knee pain a little while into her run. The pain gets progressively worse until the athlete stops running, at which point the knee pain stops almost instantly. Like with osteoarthritis, the cartilage between the thighbone and the kneecap appears to be wearing away. Previous research on PFP had focused on hip problems as possible causes for the degradation. Dierks and his team decided to test whether specific hip exercises could treat the ailment.

The scientists took a small sample of female runners. Hip strength measurements were taken at the onset of the study. For the next six weeks, the runners were given twice-weekly hip strengthening exercises, at which point hip strength measurements were repeated. Women who had begun the study feeling intense knee pain whenever they ran on a treadmill, completed the study six weeks later with little or no knee pain.

Dierks plans to run further tests to both confirm his theory about the connection between hip strength and PFP, and to improve the exercise treatment regiment, which at this point consists mainly of single-leg squats and resistance band exercises.

Tuesday, June 22, 2010

I’ve written before about some exciting work being done with human stem cells. In order to use the cells, scientists have to be able to reliably grow them under consistent conditions. To that end, Joerg Lahann, Gary Smith and their colleagues at the University of Michigan have developed a synthetic Petri dish coating.

In the past, human stem cells have been grown on a support matrix of mouse cells or mouse cell products such as Matrigel (a protein mixture made from mouse tumors). While these products adequately nourish the stem cells, they also secrete factors of their own which can have unpredictable consequences. For this reason, human stem cell lines grown using mouse products have strict therapeutic limitations.

After testing six different polymer coatings, the researchers hit upon a fully synthetic coating that was both stable and identical from batch to batch. They gave their new coating the acronym PMEDSAH. This stands for poly[2-(methacryloyloxy)ethyldimethyl(3-sulfopropyl)ammonium hydroxide], in case you were wondering. But don’t try to make it yourself, because they’ve got a patent pending.

PMEDSAH allows human stem cells to grow and, more importantly, to differentiate normally. After all, it’s the pluripotency of stem cells (their ability to become any type of cell) that makes them so useful.

Monday, June 21, 2010

Influenza is caused by a group of viruses whose genomes each contain eight separate strands of RNA. Those individual segments of RNA can not only mutate, but can also be swapped between different flu strains. In short, flu viruses are extremely variable, changing from year to year. Benjamin tenOever and his team from the Mount Sinai School of Medicine have found a novel way of attacking influenza that may result in a universal flu treatment, alleviating the need for yearly vaccines.

Each of the eight separate strands of influenza RNA encodes a viral protein. Thus, for the virus to spread, the RNA strands must undergo two distinct functions. They must be transcribed into mRNA, which the host cell obligingly uses to make viral proteins, and they must be replicated into more viral RNA strands. Together, the viral protein and RNA form new viral particles which go on to infect new cells.

A group of hitherto unknown small viral RNAs (svRNAs) was recently found within infected cells. These RNAs, each 22 to 27 nucleotides long, exactly match the 5’ ends of the eight viral RNA sections. The scientists have found that these tiny snippets of RNA are essential for the replication of the larger viral RNA strands. Depleting the svRNAs prevented viral replication, but not transcription. Remember, this means that infected cells treated with svRNA inhibitors would still be able to produce viral proteins, but that those cells would not also be full of copies of viral RNA. This is actually a potential win-win situation if the extra viral protein load triggers the host immune response without having the ability to infect new cells.

Although only at the proof of concept stage in development, tenOever and his team are optimistic that using svRNAs could lead to a whole new paradigm in flu treatment.

Sunday, June 20, 2010

Binary stars are extremely common in our galaxy, as are white dwarf stars. White dwarfs made of pure helium, on the other hand, are rare. Astrophysicists at UC Santa Barbara have identified an eclipsing binary system containing one ‘normal’ white dwarf and one helium white dwarf. The discovery enabled them to accurately measure a helium white dwarf for the first time.

White dwarfs are formed when stars below a certain size limit exhaust their fuel supplies. The end result is usually a dense core made mainly of carbon and oxygen. Helium white dwarfs, while identified over 20 years ago, are less well understood. For example, while assumed to be larger and hotter than ordinary white dwarfs, those predictions had never been confirmed experimentally. Lars Bildsten and his students at UCSB, in collaboration with Steve Howell, an astronomer at the National Optical Astronomy Observatory (NOAO) in Tucson, Arizona have now done exactly that.

The scientists had been studying a helium white dwarf designated NLTT 11748. At regular intervals, the star appeared to dim in intensity. The scientists realized that a binary partner was eclipsing the star. By carefully timing the passage of the normal star as it eclipsed the helium dwarf, the cosmologists were able to accurately measure the size of the helium white dwarf.

As predicted, NLTT 11748 is considerably larger in volume, and gives off 30 times more light than its normal white dwarf partner. Yet, the helium white dwarf has a mass just 10 to 20% of that of our sun, in contrast to its partner star, which has a mass closer to 70% of our sun.

In this artist conception of the unique binary star NLTT 11748, the larger but less massive helium white dwarf star is partially eclipsed by the smaller but more massive normal white dwarf, which is about the size of the earth.

Credit: Steve Howell/Pete Marenfeld/NOAO

As usual, astronomers like to take the long view. Bildsten says:

A particularly intriguing possibility to ponder is what will happen in 6 to 10 billion years. This binary is emitting gravitational waves at a rate that will force the two white dwarfs to make contact. What happens then is anybody's guess.

Saturday, June 19, 2010

Fluorescent tags have been used as molecular markers for decades. They have been supremely useful in literally making particular proteins light up within cells. However, they do have drawbacks, most notably that they are too big to use in certain applications. Alice Ting and her colleagues from MIT have developed a new, smaller fluorescent tag that should eliminate this problem.

The first molecular probe, known simply as green fluorescent protein (GFP), has been helping biologists identify cells and cell functions since its isolation from jellyfish in 1962. To mark proteins with GFP, the GFP gene is fused to the gene for the protein of interest. A hybrid protein is thus created which will fluoresce under the right conditions, allowing scientists to watch it go about its business in the cell. Unfortunately, at a bulky 238 amino acids, GFP can interfere with the functioning of some proteins. In addition, all parts of the cell that contain the hybrid protein will fluoresce, making it impossible to differentiate between different cell regions.

To solve these problems, the MIT team created not only a new fluorescent probe, but also a whole new method of tagging interesting proteins (PRIME-- PRobe Incorporation Mediated by Enzymes). Their new protein tagging system contains three elements. First, they developed a new smaller blue fluorescent probe (7-hydroxycoumarin). Second, they genetically altered the protein they wished to label (in this case, actin) to include a special 13 amino acid sequence. And third, they created a new enzyme (fluorophore ligase) that attaches the blue probe to the 13 amino acid protein tag. The three ingredients are mixed together in a cell, and voila! Fluorescent blue protein.

To make the new probe even more useful, Ting and her lab have been able to direct their probe to only label proteins in specific parts of the cell. They do this by attaching genetic instructions to the ligase, limiting it to certain areas of the cell.

MIT researchers have designed a fluorescent probe that can be targeted to different locations within a cell.Left, the probe only labels proteins in the cell membraneMiddle, the probe labels proteins in the cell nucleusRight, the probe labels proteins in the cytosol.Images: Katharine White and Tao Uttamapinant

Friday, June 18, 2010

Butterfly wing colors depend not on pigment within the wings but on the effect of light on microscopic structures on the wing surfaces. Although this has been understood for some time, it has been impossible to replicate the colors artificially. Mathias Kolle and his colleagues from the University of Cambridge have invented a way to manufacture the tiny color-producing structures.

Electron micrograph of natural butterfly wing: This scanning electron micrograph shows that the surface of a wing scale is covered with concavities.

Credit: Mathias Kolle, University of Cambridge

The team used the Indonesian Peacock or Swallowtail butterfly (Papilio blumei), shown above, as a model. This butterfly appears green to our naked eyes, but can become a brilliant blue under other optical conditions. The intense colors are a direct result of intricate microscopic structures. The researchers were able to successfully manufacture those vibrant colors by using nanofabrication processes, such as atomic layer deposition.

Electron micrograph of artificial structure: This SEM image of concavities is covered by a conformal multilayer stack of 11 alternating layers of titania and alumina.

Credit: Mathias Kolle, University of Cambridge

The scientists anticipate a number of uses for their new color manufacturing process, including creating optical signatures for documents and bank notes.

Wednesday, June 16, 2010

Slime molds (Dictyostelium discoideum) are amoebae that live in soil. Under normal conditions, they are single-celled organisms feeding on bacteria. However, when faced with starvation, they undergo a remarkable transformation.

The individual amoebae congregate into a multicellular slug and travel as a unit to a better location. When the slug finds a suitable spot, it transforms into a fruiting body with a clump of spores sitting atop a slender stalk. Remember, both the stalk and the spores were once free-living amoeba. Upon forming the fruiting body, the cells making up the stalk perish, whereas the cells that become spores live on. How do these jobs get divided up? Until recently, it was assumed that the first cells to run out of food would make up the stalk, whereas the cells who had the most food would become spores. In other words, the sickest cells would sacrifice themselves while the heartiest cells would continue on. It turns out, that’s completely wrong.

Jennie Kuzdzal-Fick and her mentors from Rice University carefully tracked the fates of individual D. discoideum cells as they progressed through their life cycle. To her surprise, the first cells to starve were predominantly the ones that became reproductive spores. Clearly, there is an advantage in being the first to stop eating and move into slug formation. Why, though, do the well-fed cells ‘agree’ to join the slug, only to become doomed stalk cells? The researchers are continuing to work on that question.

Tuesday, June 15, 2010

Archaeopteryx is the best-known example of the transition from land-dwelling dinosaurs to birds. Over the years, some beautiful specimens of Archaeopteryx have been found which clearly show features of both birds (feathers) and dinosaurs (teeth and bony tails). Now Roy Wogelius and his team from England’s University of Manchester and from the US Department of Energy's SLAC National Accelerator Laboratory have added chemical evidence to the proof that the animals were related to birds.

The scientists examined the Thermopolis Archaeopteryx, a very well preserved specimen that was first described in 2005. This specimen has been subjected to many noninvasive types of analysis, including CT scans. This time, the researchers used the Stanford Synchrotron Radiation Lightsource (SSRL), located at the SLAC National Accelerator Laboratory to create hair-thin, extremely bright x-ray beams. These x-rays allowed the scientists to determine the chemical make-up of the fossil.

The geochemists discovered that the feathery impressions visible in the fossil actually contain organic material, including chemical signatures of modern feathers, such as phosphorous and sulfur. Those chemicals were not found in the surrounding rock, disproving the possibility that the chemicals simply leached into the animal as it fossilized.

The authors expect this new ability to detect trace metals and chemicals in fossils to revolutionize paleontology.

Christina Roberto and her colleagues from Yale, Columbia, and the University of Cambridge, compared the brains of 32 anorexic inpatients at the Columbia University Center for Eating Disorders. The anorexic patients had less gray matter, as observed by magnetic resonance imaging (MRI), than 21 normal cohorts. The longer the women had AN, the greater the decrease in brain volume.

As the patients were treated and regained weight, their brain volumes increased. In only a couple of weeks, the patients’ gray matter was significantly restored. Researchers are not sure what sorts of cognitive effects the loss of brain volume has on people. However, they are encouraged that those effects may be reversible with proper treatment.

Sunday, June 13, 2010

Because inflammation has long been correlated with heart disease, doctors have suspected a link between poor oral hygiene, which often leads to inflammation of the mouth and gums, and cardiovascular disease. Richard Watt and his team from University College London have now documented such a link.

The researchers followed just under 5000 patients over a period of about eight years. The subjects were tested for cardiovascular health and questioned about oral hygiene habits. Those patients who self-reported rarely or never brushing their teeth had 70% more heart disease than those who said they brushed twice a day. While that’s a huge difference, remember, only a subset of patients had heart attacks during the study. The overall risk of heart disease increased from 4.2% to 7.1% for the non-brushers. So not brushing your teeth isn't a death sentence, except maybe for your social life.

The doctors aren’t sure why oral health is so tightly connected to heart health, although they suspect that the inflammation of untended gums plays an important role. The levels of C reactive protein and of fibrinogen, both of which are markers for heart disease, also increased in the non-brushing individuals.

PAHs are pernicious environmental toxins found in, to cite one example, enormous oil spills.They can cause a myriad of ill effects, ranging from cancer to reproductive and nervous system problems.There are microorganisms that can degrade PAHs, however, the PAHs must first be broken into smaller, soluble particles.

One way to help the bacterial cleanup crew is to use surfactants, also known as ‘wetting agents’ because they lower the surface tension of liquids. These agents increase the solubility and bioavailability of PAHs, which in turn allows microorganisms to degrade them. Synthetic surfactants are commonly made of petroleum and can be toxic.In contrast, biological surfactants are generally biodegradable and non-toxic.

One particular type of biological surfactant called ‘rhamnolipids’ is especially effective in degrading PAHs.Although rhamnolipids are made by many organisms, including a common bacteria called Pseudomonas aeruginosa, most of those organisms can only make it in miniscule amounts.

Enter Xihou Yin of OSU and the other researchers, who have successfully isolated a strain of P. aeruginosa from Shaanxi Province in China that can produce large amounts of 25 different rhamnolipids.With a little genetic engineering the team have increased that production rate to an extraordinary twelve grams of rhamnolipids per liter of bacteria.So far, the strain NY3 has shown tremendous promise in degrading at least five PAH compounds.The researchers plan to continue to test NY3 and hope to begin using it remove environmental pollutants.

Above: Aerial view of oil spill from Deepwater Horizon. The tiny little dot at the bottom left edge of the spill is a ship.

Previous studies have shown that when mice are injected with killed M. vaccae, their serotonin levels rise and they exhibit neural growth. Because serotonin is known to affect learning, Matthews and Jenks tried feeding live M. vaccae to mice and testing their ability to run mazes.

Mice on M. vaccae navigated mazes twice as fast as their non-bacteria eating cohorts. When weaned from the bacteria, the mice slowly lost their advantage over controls.

If this effect translates to humans, the conclusion is clear: make sure kids have plenty of time to play outside, preferably making mud pies.

Thursday, June 10, 2010

Okay, it’s not actually going anywhere. The Mars 500 mission is a simulation of a voyage to Mars. Back in November, six participants from Russia, Europe and China were chosen to spend a total of 520 days in a test facility at the Moscow Institute of Biomedical Problems in Moscow. A real journey to Mars is expected to take 250 days out and 240 days back (because of the position of the orbits). Those of you doing the math will notice that the crew will have an extra 30 days between the two trips to pretend to cavort across the surface of Mars.

Although they won’t be simulating weightlessness or radiation exposure, they will have to deal with isolation, boredom, and any emergencies that might arise with their food supplies, equipment or medical conditions. During the 520 days, the volunteers will take a wide assortment of tests on their physical, cognitive and mental health.

Wednesday, June 9, 2010

Were the dinosaurs warm blooded or cold blooded? Thanks to scientists from Caltech, UCLA, Universität Bonn and the University of Florida, we’re close to having that answer. They’ve discovered a way to reliably take the internal temperature of fossilized animals.

The trick was to look for clusters of the isotopes carbon-13 (13C)and oxygen-18 (18O). As new bone is created in living vertebrates, carbon and oxygen (among other elements) precipitate out of the bloodstream and harden into bioapatite, or mineralized bone. A fraction of the carbon and oxygen will be 13C and 18O. Now here’s the interesting part: those two isotopes will be clumped together if they were deposited at lower temperatures, but spread more randomly through the bioapatite if they were deposited at higher temperatures.

The scientists have tested their concept by looking at the bioapatite of living animals. They then examined the teeth of mammoths and extinct rhinos (mammals with a high internal temperature) and an extinct relative of the alligator (a reptile with a low internal temperature). Thus far, the isotope clumping data correlates well with the expected internal temperatures of the animals.

The researchers plan to start examining dinosaur eggshells and teeth next. Aside from learning some interesting things about dinosaurs, the new data could yield important information about the evolution of birds.

As John Eiler of Caltech says:

Were [birds] warm-blooded before or after they started to fly? Before or after they developed feathers?

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.